==3123834== Memcheck, a memory error detector
==3123834== Copyright (C) 2002-2026, and GNU GPL'd, by Julian Seward et al.
==3123834== Using Valgrind-3.27.1 and LibVEX; rerun with -h for copyright info
==3123834== Command: /data/localhost/ripley/R/R-devel-vg/bin/exec/R --vanilla
==3123834== 

R Under development (unstable) (2026-07-29 r90317) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> pkgname <- "secrfunc"
> source(file.path(R.home("share"), "R", "examples-header.R"))
> options(warn = 1)
> library('secrfunc')
> 
> base::assign(".oldSearch", base::search(), pos = 'CheckExEnv')
> base::assign(".old_wd", base::getwd(), pos = 'CheckExEnv')
> cleanEx()
> nameEx("hdotpolycpp")
> ### * hdotpolycpp
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: hdotpolycpp
> ### Title: Net Detection Hazard for Polygon and Transect Detectors
> ### Aliases: hdotpolycpp
> 
> ### ** Examples
> 
> 
> set.seed(123)
> 
> # 50 random points
> xy <- matrix(runif(100), ncol = 2) * 2 - 1
> 
> # centred unit polygon 
> traps <- matrix(c(0,0,1,1,0,0,1,1,0,0), ncol = 2) - 0.5
> 
> Tsk <- matrix(1, nrow = 1, ncol = 5)
> markocc <- rep(1,5)
> cumk <- c(0,5,0)   # zero-terminated
> detectfn <- 14   # hazard half-normal
> gsb <- c(lambda0 = 0.2, sigma = 0.5)
> 
> h <- hdotpolycpp(xy, traps, Tsk, markocc, cumk, detectfn, gsb, 
+     convex = TRUE, dim = 2, grain = 1, ncores = 2)
==3123834== Invalid read of size 8
==3123834==    at 0x1245B76F: hdotpoly::operator()(unsigned long, unsigned long) (/data/localhost/ripley/R/packages/tests-vg/secrfunc/src/hdot.cpp:73)
==3123834==    by 0xBF2AB6E: operator() (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/tbb.cpp:23)
==3123834==    by 0xBF2AB6E: __invoke_impl<void, const RcppParallel::TBBWorker&, tbb::detail::d1::blocked_range<long unsigned int>&> (/usr/include/c++/16/bits/invoke.h:63)
==3123834==    by 0xBF2AB6E: __invoke<const RcppParallel::TBBWorker&, tbb::detail::d1::blocked_range<long unsigned int>&> (/usr/include/c++/16/bits/invoke.h:98)
==3123834==    by 0xBF2AB6E: invoke<const RcppParallel::TBBWorker&, tbb::detail::d1::blocked_range<long unsigned int>&> (/usr/include/c++/16/functional:126)
==3123834==    by 0xBF2AB6E: invoke<const RcppParallel::TBBWorker&, tbb::detail::d1::blocked_range<long unsigned int>&> (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/../inst/include/tbb/../oneapi/tbb/detail/_utils.h:356)
==3123834==    by 0xBF2AB6E: run_body (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/../inst/include/tbb/../oneapi/tbb/parallel_for.h:117)
==3123834==    by 0xBF2AB6E: void tbb::detail::d1::dynamic_grainsize_mode<tbb::detail::d1::adaptive_mode<tbb::detail::d1::auto_partition_type> >::work_balance<tbb::detail::d1::start_for<tbb::detail::d1::blocked_range<unsigned long>, RcppParallel::TBBWorker, tbb::detail::d1::auto_partitioner const>, tbb::detail::d1::blocked_range<unsigned long> >(tbb::detail::d1::start_for<tbb::detail::d1::blocked_range<unsigned long>, RcppParallel::TBBWorker, tbb::detail::d1::auto_partitioner const>&, tbb::detail::d1::blocked_range<unsigned long>&, tbb::detail::d1::execution_data&) (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/../inst/include/tbb/../oneapi/tbb/partitioner.h:450)
==3123834==    by 0xBF2AF77: execute<tbb::detail::d1::start_for<tbb::detail::d1::blocked_range<long unsigned int>, RcppParallel::TBBWorker, const tbb::detail::d1::auto_partitioner>, tbb::detail::d1::blocked_range<long unsigned int> > (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/../inst/include/tbb/../oneapi/tbb/partitioner.h:289)
==3123834==    by 0xBF2AF77: tbb::detail::d1::start_for<tbb::detail::d1::blocked_range<unsigned long>, RcppParallel::TBBWorker, tbb::detail::d1::auto_partitioner const>::execute(tbb::detail::d1::execution_data&) (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/../inst/include/tbb/../oneapi/tbb/parallel_for.h:170)
==3123834==    by 0x12084C52: local_wait_for_all<false, tbb::detail::r1::external_waiter> (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/tbb/src/tbb/task_dispatcher.h:334)
==3123834==    by 0x12084C52: local_wait_for_all<tbb::detail::r1::external_waiter> (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/tbb/src/tbb/task_dispatcher.h:470)
==3123834==    by 0x12084C52: tbb::detail::r1::task_dispatcher::execute_and_wait(tbb::detail::d1::task*, tbb::detail::d1::wait_context&, tbb::detail::d1::task_group_context&) (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/tbb/src/tbb/task_dispatcher.cpp:168)
==3123834==    by 0xBF29220: execute_and_wait (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/../inst/include/tbb/../oneapi/tbb/detail/_task.h:262)
==3123834==    by 0xBF29220: run (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/../inst/include/tbb/../oneapi/tbb/parallel_for.h:112)
==3123834==    by 0xBF29220: run (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/../inst/include/tbb/../oneapi/tbb/parallel_for.h:104)
==3123834==    by 0xBF29220: run (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/../inst/include/tbb/../oneapi/tbb/parallel_for.h:101)
==3123834==    by 0xBF29220: parallel_for<tbb::detail::d1::blocked_range<long unsigned int>, RcppParallel::TBBWorker> (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/../inst/include/tbb/../oneapi/tbb/parallel_for.h:229)
==3123834==    by 0xBF29220: operator() (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/tbb.cpp:72)
==3123834==    by 0xBF29220: task_ptr_or_nullptr<const RcppParallel::TBBParallelForExecutor&> (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/../inst/include/tbb/../oneapi/tbb/task_group.h:131)
==3123834==    by 0xBF29220: tbb::detail::d2::function_stack_task<RcppParallel::TBBParallelForExecutor>::execute(tbb::detail::d1::execution_data&) (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/../inst/include/tbb/../oneapi/tbb/task_group.h:451)
==3123834==    by 0x12084C52: local_wait_for_all<false, tbb::detail::r1::external_waiter> (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/tbb/src/tbb/task_dispatcher.h:334)
==3123834==    by 0x12084C52: local_wait_for_all<tbb::detail::r1::external_waiter> (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/tbb/src/tbb/task_dispatcher.h:470)
==3123834==    by 0x12084C52: tbb::detail::r1::task_dispatcher::execute_and_wait(tbb::detail::d1::task*, tbb::detail::d1::wait_context&, tbb::detail::d1::task_group_context&) (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/tbb/src/tbb/task_dispatcher.cpp:168)
==3123834==    by 0xBF2891D: execute_and_wait (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/../inst/include/tbb/../oneapi/tbb/detail/_task.h:262)
==3123834==    by 0xBF2891D: operator() (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/../inst/include/tbb/../oneapi/tbb/task_group.h:476)
==3123834==    by 0xBF2891D: on_completion<tbb::detail::d2::task_group_base::internal_run_and_wait<RcppParallel::TBBParallelForExecutor>(const RcppParallel::TBBParallelForExecutor&)::<lambda()> > (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/../inst/include/tbb/../oneapi/tbb/detail/_template_helpers.h:230)
==3123834==    by 0xBF2891D: internal_run_and_wait<RcppParallel::TBBParallelForExecutor> (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/../inst/include/tbb/../oneapi/tbb/task_group.h:477)
==3123834==    by 0xBF2891D: run_and_wait<RcppParallel::TBBParallelForExecutor> (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/../inst/include/tbb/../oneapi/tbb/task_group.h:595)
==3123834==    by 0xBF2891D: operator() (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/tbb.cpp:105)
==3123834==    by 0xBF2891D: tbb::detail::d1::task_arena_function<RcppParallel::TBBArenaParallelForExecutor, void>::operator()() const (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/../inst/include/tbb/../oneapi/tbb/task_arena.h:68)
==3123834==    by 0x120703E2: tbb::detail::r1::task_arena_impl::execute(tbb::detail::d1::task_arena_base&, tbb::detail::d1::delegate_base&) (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/tbb/src/tbb/arena.cpp:821)
==3123834==    by 0xBF27EE3: execute_impl<void, RcppParallel::TBBArenaParallelForExecutor> (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/../inst/include/tbb/../oneapi/tbb/task_arena.h:251)
==3123834==    by 0xBF27EE3: execute<RcppParallel::TBBArenaParallelForExecutor&> (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/../inst/include/tbb/../oneapi/tbb/task_arena.h:404)
==3123834==    by 0xBF27EE3: RcppParallel::tbbParallelFor(unsigned long, unsigned long, RcppParallel::Worker&, unsigned long, int) (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/tbb.cpp:129)
==3123834==    by 0x1245A992: hdotpolycpp(Rcpp::Matrix<14, Rcpp::PreserveStorage> const&, Rcpp::Matrix<14, Rcpp::PreserveStorage> const&, Rcpp::Matrix<14, Rcpp::PreserveStorage> const&, Rcpp::Vector<13, Rcpp::PreserveStorage> const&, Rcpp::Vector<13, Rcpp::PreserveStorage> const&, int const&, Rcpp::Vector<14, Rcpp::PreserveStorage> const&, bool const&, int const&, int const&, int const&) (/data/localhost/ripley/R/packages/tests-vg/secrfunc/src/hdot.cpp:115)
==3123834==    by 0x12447D45: _secrfunc_hdotpolycpp (/data/localhost/ripley/R/packages/tests-vg/secrfunc/src/RcppExports.cpp:31)
==3123834==    by 0x496C93: R_doDotCall (/data/localhost/ripley/R/svn/R-devel/src/main/dotcode.c:801)
==3123834==  Address 0x8b5d500 is 1,104 bytes inside a block of size 7,960 alloc'd
==3123834==    at 0x4840AE6: malloc (/builddir/build/BUILD/valgrind-3.27.1-build/valgrind-3.27.1/coregrind/m_replacemalloc/vg_replace_malloc.c:447)
==3123834==    by 0x5296F9: GetNewPage (/data/localhost/ripley/R/svn/R-devel/src/main/memory.c:998)
==3123834==    by 0x52B773: Rf_allocVector3 (/data/localhost/ripley/R/svn/R-devel/src/main/memory.c:2872)
==3123834==    by 0x4A01AF: Rf_allocVector (/data/localhost/ripley/R/svn/R-devel/src/include/Rinlinedfuns.h:609)
==3123834==    by 0x4A01AF: duplicate1 (/data/localhost/ripley/R/svn/R-devel/src/main/duplicate.c:359)
==3123834==    by 0x5C339C: match5 (/data/localhost/ripley/R/svn/R-devel/src/main/unique.c:1383)
==3123834==    by 0x4D8F5D: bcEval_loop (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:8150)
==3123834==    by 0x4E40E1: bcEval (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7533)
==3123834==    by 0x4E40E1: bcEval (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7518)
==3123834==    by 0x4E44AA: Rf_eval (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1167)
==3123834==    by 0x4E6346: R_execClosure (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2398)
==3123834==    by 0x4E70EF: applyClosure_core (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2314)
==3123834==    by 0x4E46B8: Rf_applyClosure (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2333)
==3123834==    by 0x4E46B8: Rf_eval (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1278)
==3123834==    by 0x4E9569: do_set (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:3585)
==3123834== 
==3123834== Invalid read of size 8
==3123834==    at 0x1245B76F: hdotpoly::operator()(unsigned long, unsigned long) (/data/localhost/ripley/R/packages/tests-vg/secrfunc/src/hdot.cpp:73)
==3123834==    by 0xBF2AF77: execute<tbb::detail::d1::start_for<tbb::detail::d1::blocked_range<long unsigned int>, RcppParallel::TBBWorker, const tbb::detail::d1::auto_partitioner>, tbb::detail::d1::blocked_range<long unsigned int> > (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/../inst/include/tbb/../oneapi/tbb/partitioner.h:289)
==3123834==    by 0xBF2AF77: tbb::detail::d1::start_for<tbb::detail::d1::blocked_range<unsigned long>, RcppParallel::TBBWorker, tbb::detail::d1::auto_partitioner const>::execute(tbb::detail::d1::execution_data&) (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/../inst/include/tbb/../oneapi/tbb/parallel_for.h:170)
==3123834==    by 0x12084C52: local_wait_for_all<false, tbb::detail::r1::external_waiter> (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/tbb/src/tbb/task_dispatcher.h:334)
==3123834==    by 0x12084C52: local_wait_for_all<tbb::detail::r1::external_waiter> (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/tbb/src/tbb/task_dispatcher.h:470)
==3123834==    by 0x12084C52: tbb::detail::r1::task_dispatcher::execute_and_wait(tbb::detail::d1::task*, tbb::detail::d1::wait_context&, tbb::detail::d1::task_group_context&) (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/tbb/src/tbb/task_dispatcher.cpp:168)
==3123834==    by 0xBF29220: execute_and_wait (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/../inst/include/tbb/../oneapi/tbb/detail/_task.h:262)
==3123834==    by 0xBF29220: run (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/../inst/include/tbb/../oneapi/tbb/parallel_for.h:112)
==3123834==    by 0xBF29220: run (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/../inst/include/tbb/../oneapi/tbb/parallel_for.h:104)
==3123834==    by 0xBF29220: run (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/../inst/include/tbb/../oneapi/tbb/parallel_for.h:101)
==3123834==    by 0xBF29220: parallel_for<tbb::detail::d1::blocked_range<long unsigned int>, RcppParallel::TBBWorker> (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/../inst/include/tbb/../oneapi/tbb/parallel_for.h:229)
==3123834==    by 0xBF29220: operator() (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/tbb.cpp:72)
==3123834==    by 0xBF29220: task_ptr_or_nullptr<const RcppParallel::TBBParallelForExecutor&> (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/../inst/include/tbb/../oneapi/tbb/task_group.h:131)
==3123834==    by 0xBF29220: tbb::detail::d2::function_stack_task<RcppParallel::TBBParallelForExecutor>::execute(tbb::detail::d1::execution_data&) (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/../inst/include/tbb/../oneapi/tbb/task_group.h:451)
==3123834==    by 0x12084C52: local_wait_for_all<false, tbb::detail::r1::external_waiter> (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/tbb/src/tbb/task_dispatcher.h:334)
==3123834==    by 0x12084C52: local_wait_for_all<tbb::detail::r1::external_waiter> (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/tbb/src/tbb/task_dispatcher.h:470)
==3123834==    by 0x12084C52: tbb::detail::r1::task_dispatcher::execute_and_wait(tbb::detail::d1::task*, tbb::detail::d1::wait_context&, tbb::detail::d1::task_group_context&) (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/tbb/src/tbb/task_dispatcher.cpp:168)
==3123834==    by 0xBF2891D: execute_and_wait (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/../inst/include/tbb/../oneapi/tbb/detail/_task.h:262)
==3123834==    by 0xBF2891D: operator() (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/../inst/include/tbb/../oneapi/tbb/task_group.h:476)
==3123834==    by 0xBF2891D: on_completion<tbb::detail::d2::task_group_base::internal_run_and_wait<RcppParallel::TBBParallelForExecutor>(const RcppParallel::TBBParallelForExecutor&)::<lambda()> > (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/../inst/include/tbb/../oneapi/tbb/detail/_template_helpers.h:230)
==3123834==    by 0xBF2891D: internal_run_and_wait<RcppParallel::TBBParallelForExecutor> (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/../inst/include/tbb/../oneapi/tbb/task_group.h:477)
==3123834==    by 0xBF2891D: run_and_wait<RcppParallel::TBBParallelForExecutor> (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/../inst/include/tbb/../oneapi/tbb/task_group.h:595)
==3123834==    by 0xBF2891D: operator() (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/tbb.cpp:105)
==3123834==    by 0xBF2891D: tbb::detail::d1::task_arena_function<RcppParallel::TBBArenaParallelForExecutor, void>::operator()() const (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/../inst/include/tbb/../oneapi/tbb/task_arena.h:68)
==3123834==    by 0x120703E2: tbb::detail::r1::task_arena_impl::execute(tbb::detail::d1::task_arena_base&, tbb::detail::d1::delegate_base&) (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/tbb/src/tbb/arena.cpp:821)
==3123834==    by 0xBF27EE3: execute_impl<void, RcppParallel::TBBArenaParallelForExecutor> (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/../inst/include/tbb/../oneapi/tbb/task_arena.h:251)
==3123834==    by 0xBF27EE3: execute<RcppParallel::TBBArenaParallelForExecutor&> (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/../inst/include/tbb/../oneapi/tbb/task_arena.h:404)
==3123834==    by 0xBF27EE3: RcppParallel::tbbParallelFor(unsigned long, unsigned long, RcppParallel::Worker&, unsigned long, int) (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/tbb.cpp:129)
==3123834==    by 0x1245A992: hdotpolycpp(Rcpp::Matrix<14, Rcpp::PreserveStorage> const&, Rcpp::Matrix<14, Rcpp::PreserveStorage> const&, Rcpp::Matrix<14, Rcpp::PreserveStorage> const&, Rcpp::Vector<13, Rcpp::PreserveStorage> const&, Rcpp::Vector<13, Rcpp::PreserveStorage> const&, int const&, Rcpp::Vector<14, Rcpp::PreserveStorage> const&, bool const&, int const&, int const&, int const&) (/data/localhost/ripley/R/packages/tests-vg/secrfunc/src/hdot.cpp:115)
==3123834==    by 0x12447D45: _secrfunc_hdotpolycpp (/data/localhost/ripley/R/packages/tests-vg/secrfunc/src/RcppExports.cpp:31)
==3123834==    by 0x496C93: R_doDotCall (/data/localhost/ripley/R/svn/R-devel/src/main/dotcode.c:801)
==3123834==    by 0x4D4C18: bcEval_loop (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:8700)
==3123834==  Address 0x8b5d500 is 1,104 bytes inside a block of size 7,960 alloc'd
==3123834==    at 0x4840AE6: malloc (/builddir/build/BUILD/valgrind-3.27.1-build/valgrind-3.27.1/coregrind/m_replacemalloc/vg_replace_malloc.c:447)
==3123834==    by 0x5296F9: GetNewPage (/data/localhost/ripley/R/svn/R-devel/src/main/memory.c:998)
==3123834==    by 0x52B773: Rf_allocVector3 (/data/localhost/ripley/R/svn/R-devel/src/main/memory.c:2872)
==3123834==    by 0x4A01AF: Rf_allocVector (/data/localhost/ripley/R/svn/R-devel/src/include/Rinlinedfuns.h:609)
==3123834==    by 0x4A01AF: duplicate1 (/data/localhost/ripley/R/svn/R-devel/src/main/duplicate.c:359)
==3123834==    by 0x5C339C: match5 (/data/localhost/ripley/R/svn/R-devel/src/main/unique.c:1383)
==3123834==    by 0x4D8F5D: bcEval_loop (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:8150)
==3123834==    by 0x4E40E1: bcEval (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7533)
==3123834==    by 0x4E40E1: bcEval (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7518)
==3123834==    by 0x4E44AA: Rf_eval (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1167)
==3123834==    by 0x4E6346: R_execClosure (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2398)
==3123834==    by 0x4E70EF: applyClosure_core (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2314)
==3123834==    by 0x4E46B8: Rf_applyClosure (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2333)
==3123834==    by 0x4E46B8: Rf_eval (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1278)
==3123834==    by 0x4E9569: do_set (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:3585)
==3123834== 
> 
> 
> 
> 
> cleanEx()
> nameEx("makegkPolygoncpp")
> ### * makegkPolygoncpp
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: makegkPolygoncpp
> ### Title: Pre-compute Detection Hazard
> ### Aliases: makegkPolygoncpp
> 
> ### ** Examples
> 
> 
> detectfn <- 14   # hazard half-normal
> dim <- 2
> convex <- TRUE
> grain <- 1
> ncores <- 2
> # for a single parameter combination
> gsbval <- matrix(c(0.2,1), nrow = 1)
> cumk <- c(0,5)   
> # centred unit polygon 
> traps <- matrix(c(0,0,1,1,0,0,1,1,0,0), ncol = 2) - 0.5
> mask <- as.matrix(expand.grid(x=-2:2, y=-2:2))
> 
> makegkPolygoncpp(detectfn, dim, convex, grain, ncores, gsbval, cumk, traps, mask)
$H
[1] 1.256637

$gk
 [1] 0.0007341427 0.0029253653 0.0046301092 0.0029253653 0.0007341427
 [6] 0.0029253653 0.0116186869 0.0183426028 0.0116186869 0.0029253653
[11] 0.0046301092 0.0183426028 0.0289004563 0.0183426028 0.0046301092
[16] 0.0029253653 0.0116186869 0.0183426028 0.0116186869 0.0029253653
[21] 0.0007341427 0.0029253653 0.0046301092 0.0029253653 0.0007341427

$hk
 [1] 0.0007344123 0.0029296526 0.0046408614 0.0029296526 0.0007344123
 [6] 0.0029296526 0.0116867112 0.0185129141 0.0116867112 0.0029296526
[11] 0.0046408614 0.0185129141 0.0293262993 0.0185129141 0.0046408614
[16] 0.0029296526 0.0116867112 0.0185129141 0.0116867112 0.0029296526
[21] 0.0007344123 0.0029296526 0.0046408614 0.0029296526 0.0007344123

> 
> 
> 
> 
> cleanEx()
> nameEx("polygonhistoriescpp")
> ### * polygonhistoriescpp
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: polygonhistoriescpp
> ### Title: Probability of Polygon Capture Histories
> ### Aliases: polygonhistoriescpp polygonfxicpp
> 
> ### ** Examples
> 
> 
> datafilename <- system.file("extdata/testdata.RData", package = "secrfunc")
> load(datafilename)  # loads w, dimw, xy, start, traps, mask, gsbval, cumk, binomN
> 
> detectfn <- 14   # hazard half-normal
> dim <- 2
> convex <- TRUE
> grain <- 1
> ncores <- 2
> 
> gkhk <- makegkPolygoncpp(detectfn, dim, convex, grain, ncores, gsbval, cumk, traps, mask)
> # see tests for expected result
> 
> nc      <- dimw[1]  # individuals
> S       <- dimw[2]  # occasions
> K       <- dimw[3]  # single polygon
> minp    <- 1e-200
> group   <- rep(0,nc)
> pID     <- matrix(1, nrow = S, ncol = 1)
> density <- matrix(1/nrow(mask), nrow(mask), 1)
> PIA     <- as.integer(array (1, dim = c(nc, S, K)))
> Tsk     <- matrix(1, nrow = K, ncol = S)
> h       <- matrix(-1)
> hindex  <- matrix(-1)
> debug   <- FALSE
> 
> prw <- polygonhistoriescpp(nc, detectfn, grain, ncores, minp, binomN, w, xy, start, 
+     group, gkhk$hk, gkhk$H, gsbval, pID, mask, density, PIA, Tsk, h, hindex, debug)
> # see tests for expected result
> 
> fxi <- polygonfxicpp(nc, detectfn, grain, ncores, minp, binomN, w, xy, start, 
+     group, gkhk$hk, gkhk$H, gsbval, pID, mask, density, PIA, Tsk, h, hindex)
> # see tests for expected result
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  40.727 0.434 41.426 0.01 0.038 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
==3123834== 
==3123834== HEAP SUMMARY:
==3123834==     in use at exit: 63,208,655 bytes in 12,743 blocks
==3123834==   total heap usage: 1,193,681 allocs, 1,180,938 frees, 764,114,230 bytes allocated
==3123834== 
==3123834== 384 bytes in 1 blocks are possibly lost in loss record 143 of 1,609
==3123834==    at 0x484862B: calloc (/builddir/build/BUILD/valgrind-3.27.1-build/valgrind-3.27.1/coregrind/m_replacemalloc/vg_replace_malloc.c:1616)
==3123834==    by 0x40120BF: calloc (/usr/src/debug/glibc-2.43-7.fc44.x86_64/elf/../include/rtld-malloc.h:44)
==3123834==    by 0x40120BF: allocate_dtv (/usr/src/debug/glibc-2.43-7.fc44.x86_64/elf/../elf/dl-tls.c:470)
==3123834==    by 0x4012B81: _dl_allocate_tls (/usr/src/debug/glibc-2.43-7.fc44.x86_64/elf/../elf/dl-tls.c:722)
==3123834==    by 0x56CF9CE: allocate_stack (/usr/src/debug/glibc-2.43-7.fc44.x86_64/nptl/allocatestack.c:568)
==3123834==    by 0x56CF9CE: pthread_create@@GLIBC_2.34 (/usr/src/debug/glibc-2.43-7.fc44.x86_64/nptl/pthread_create.c:680)
==3123834==    by 0x1207B934: launch (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/tbb/src/tbb/rml_thread_monitor.h:208)
==3123834==    by 0x1207B934: wake_or_launch (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/tbb/src/tbb/private_server.cpp:305)
==3123834==    by 0x1207B934: tbb::detail::r1::rml::private_server::wake_some(int) (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/tbb/src/tbb/private_server.cpp:412)
==3123834==    by 0x12081994: adjust_job_count_estimate (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/tbb/src/tbb/private_server.cpp:423)
==3123834==    by 0x12081994: adjust_job_count_estimate (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/tbb/src/tbb/thread_dispatcher.cpp:180)
==3123834==    by 0x12081994: tbb::detail::r1::thread_request_serializer::update(int) (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/tbb/src/tbb/thread_request_serializer.cpp:42)
==3123834==    by 0x1207B2ED: update (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/tbb/src/tbb/thread_request_serializer.cpp:113)
==3123834==    by 0x1207B2ED: notify_thread_request (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/tbb/src/tbb/permit_manager.h:49)
==3123834==    by 0x1207B2ED: notify_thread_request (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/tbb/src/tbb/permit_manager.h:46)
==3123834==    by 0x1207B2ED: tbb::detail::r1::market::adjust_demand(tbb::detail::r1::pm_client&, int, int) (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/tbb/src/tbb/market.cpp:138)
==3123834==    by 0x1207DD1C: adjust_demand (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/tbb/src/tbb/threading_control.cpp:164)
==3123834==    by 0x1207DD1C: adjust_demand (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/tbb/src/tbb/threading_control.cpp:398)
==3123834==    by 0x1207DD1C: request_workers (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/tbb/src/tbb/arena.cpp:343)
==3123834==    by 0x1207DD1C: advertise_new_work<(tbb::detail::r1::arena::new_work_type)1> (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/tbb/src/tbb/arena.h:436)
==3123834==    by 0x1207DD1C: void tbb::detail::r1::arena::advertise_new_work<(tbb::detail::r1::arena::new_work_type)0>() (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/tbb/src/tbb/arena.h:405)
==3123834==    by 0xBF2B098: spawn (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/../inst/include/tbb/../oneapi/tbb/detail/_task.h:253)
==3123834==    by 0xBF2B098: spawn_task (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/../inst/include/tbb/../oneapi/tbb/partitioner.h:499)
==3123834==    by 0xBF2B098: spawn_self (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/../inst/include/tbb/../oneapi/tbb/parallel_for.h:144)
==3123834==    by 0xBF2B098: offer_work_impl<tbb::detail::d1::start_for<tbb::detail::d1::blocked_range<long unsigned int>, RcppParallel::TBBWorker, const tbb::detail::d1::auto_partitioner>&, tbb::detail::d0::split&> (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/../inst/include/tbb/../oneapi/tbb/parallel_for.h:140)
==3123834==    by 0xBF2B098: offer_work (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/../inst/include/tbb/../oneapi/tbb/parallel_for.h:122)
==3123834==    by 0xBF2B098: execute<tbb::detail::d1::start_for<tbb::detail::d1::blocked_range<long unsigned int>, RcppParallel::TBBWorker, const tbb::detail::d1::auto_partitioner>, tbb::detail::d1::blocked_range<long unsigned int> > (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/../inst/include/tbb/../oneapi/tbb/partitioner.h:285)
==3123834==    by 0xBF2B098: tbb::detail::d1::start_for<tbb::detail::d1::blocked_range<unsigned long>, RcppParallel::TBBWorker, tbb::detail::d1::auto_partitioner const>::execute(tbb::detail::d1::execution_data&) (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/../inst/include/tbb/../oneapi/tbb/parallel_for.h:170)
==3123834==    by 0x12084C52: local_wait_for_all<false, tbb::detail::r1::external_waiter> (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/tbb/src/tbb/task_dispatcher.h:334)
==3123834==    by 0x12084C52: local_wait_for_all<tbb::detail::r1::external_waiter> (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/tbb/src/tbb/task_dispatcher.h:470)
==3123834==    by 0x12084C52: tbb::detail::r1::task_dispatcher::execute_and_wait(tbb::detail::d1::task*, tbb::detail::d1::wait_context&, tbb::detail::d1::task_group_context&) (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/tbb/src/tbb/task_dispatcher.cpp:168)
==3123834==    by 0xBF29220: execute_and_wait (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/../inst/include/tbb/../oneapi/tbb/detail/_task.h:262)
==3123834==    by 0xBF29220: run (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/../inst/include/tbb/../oneapi/tbb/parallel_for.h:112)
==3123834==    by 0xBF29220: run (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/../inst/include/tbb/../oneapi/tbb/parallel_for.h:104)
==3123834==    by 0xBF29220: run (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/../inst/include/tbb/../oneapi/tbb/parallel_for.h:101)
==3123834==    by 0xBF29220: parallel_for<tbb::detail::d1::blocked_range<long unsigned int>, RcppParallel::TBBWorker> (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/../inst/include/tbb/../oneapi/tbb/parallel_for.h:229)
==3123834==    by 0xBF29220: operator() (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/tbb.cpp:72)
==3123834==    by 0xBF29220: task_ptr_or_nullptr<const RcppParallel::TBBParallelForExecutor&> (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/../inst/include/tbb/../oneapi/tbb/task_group.h:131)
==3123834==    by 0xBF29220: tbb::detail::d2::function_stack_task<RcppParallel::TBBParallelForExecutor>::execute(tbb::detail::d1::execution_data&) (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/../inst/include/tbb/../oneapi/tbb/task_group.h:451)
==3123834==    by 0x12084C52: local_wait_for_all<false, tbb::detail::r1::external_waiter> (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/tbb/src/tbb/task_dispatcher.h:334)
==3123834==    by 0x12084C52: local_wait_for_all<tbb::detail::r1::external_waiter> (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/tbb/src/tbb/task_dispatcher.h:470)
==3123834==    by 0x12084C52: tbb::detail::r1::task_dispatcher::execute_and_wait(tbb::detail::d1::task*, tbb::detail::d1::wait_context&, tbb::detail::d1::task_group_context&) (/tmp/Rtmp2whG57/R.INSTALL3dbb5d2d0463de/RcppParallel/src/tbb/src/tbb/task_dispatcher.cpp:168)
==3123834== 
==3123834== LEAK SUMMARY:
==3123834==    definitely lost: 0 bytes in 0 blocks
==3123834==    indirectly lost: 0 bytes in 0 blocks
==3123834==      possibly lost: 384 bytes in 1 blocks
==3123834==    still reachable: 63,208,271 bytes in 12,742 blocks
==3123834==         suppressed: 0 bytes in 0 blocks
==3123834== Reachable blocks (those to which a pointer was found) are not shown.
==3123834== To see them, rerun with: --leak-check=full --show-leak-kinds=all
==3123834== 
==3123834== For lists of detected and suppressed errors, rerun with: -s
==3123834== ERROR SUMMARY: 51 errors from 3 contexts (suppressed: 0 from 0)